Gut microbiota density influences host physiology and is shaped by host and microbial factors

Eduardo J. Contijoch, Graham J. Britton, Chao Yang, Ilaria Mogno, Zhihua Li, Ruby Ng, Sean R. Llewellyn, Sheela Hira, Crystal Johnson, Keren M. Rabinowitz, Revital Barkan, Iris Dotan, Robert P. Hirten, Shih Chen Fu, Yuying Luo, Nancy Yang, Tramy Luong, Philippe R. Labrias, Sergio Lira, Inga PeterAri Grinspan, Jose C. Clemente, Roman Kosoy, Seunghee Kim-Schulze, Xiaochen Qin, Anabella Castillo, Amanda Hurley, Ashish Atreja, Jason Rogers, Farah Fasihuddin, Merjona Saliaj, Amy Nolan, Pamela Reyes-Mercedes, Carina Rodriguez, Sarah Aly, Kenneth Santa-Cruz, Lauren Peters, Mayte Suárez-Fariñas, Ruiqi Huang, Ke Hao, Jun Zhu, Bin Zhang, Bojan Losic, Haritz Irizar, Won Min Song, Antonio Di Narzo, Wenhui Wang, Benjamin L. Cohen, Christopher Dimaio, David Greenwald, Steven Itzkowitz, Aimee Lucas, James Marion, Elana Maser, Ryan Ungaro, Steven Naymagon, Joshua Novak, Brijen Shah, Thomas Ullman, Peter Rubin, James George, Peter Legnani, Shannon E. Telesco, Joshua R. Friedman, Carrie Brodmerkel, Scott Plevy, Judy H. Cho, Jean Frederic Colombel, Eric E. Schadt, Carmen Argmann, Marla Dubinsky, Andrew Kasarskis, Bruce Sands, Jeremiah J. Faith*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

102 Scopus citations


To identify factors that regulate gut microbiota density and the impact of varied microbiota density on health, we assayed this fundamental ecosystem property in fecal samples across mammals, human disease, and therapeutic interventions. Physiologic features of the host (carrying capacity) and the fitness of the gut microbiota shape microbiota density. Therapeutic manipulation of microbiota density in mice altered host metabolic and immune homeostasis. In humans, gut microbiota density was reduced in Crohn’s disease, ulcerative colitis, and ileal pouch-anal anastomosis. The gut microbiota in recurrent Clostridium difficile infection had lower density and reduced fitness that were restored by fecal microbiota transplantation. Understanding the interplay between microbiota and disease in terms of microbiota density, host carrying capacity, and microbiota fitness provide new insights into microbiome structure and microbiome targeted therapeutics.

Original languageEnglish
Article numbere40553
StatePublished - 2019


FundersFunder number
Cancer Center SupportP30CA016087
National Institute of Diabetes and Digestive and Kidney DiseasesF31DK112679
National Institute of Diabetes and Digestive and Kidney Diseases
Icahn School of Medicine at Mount SinaiPRJNA413199
Icahn School of Medicine at Mount Sinai
Stanford Genome Technology Center


    Dive into the research topics of 'Gut microbiota density influences host physiology and is shaped by host and microbial factors'. Together they form a unique fingerprint.

    Cite this